[gmx-users] Water molecule can not be settled - mdrun error

[Peter C. Lai]

Then yes, your cutoffs are still wrong. However check to see if atom 8376 is
clashing with something nearby (protein?). You also never gave any data about
the result of the previous energy minimization steps...

On 2012-09-24 04:54:13PM +0100, Lara Bunte wrote:
> Hi Peter
> 
> My complete .mdp file is now:
> 
> define          = -DPOSRES
> 
> integrator      = md
> dt              = 0.002
> emtol           = 1000.0        
> emstep          = 0.01          
> nsteps          = 5000          
> 
> nstlist         = 1             
> rlist           = 1.5            
> rlistlong       = 1.4           
> rcoulomb        = 1.5           
> coulombtype     = pme
> vdw-type        = switch
> rvdw_switch     = 0.8
> rvdw            = 1.5           
> 
> nstxout         = 100           
> nstvout         = 100           
> nstenergy       = 100           
> nstlog          = 100           
> 
> tcoupl          = V-rescale     
> tc-grps         = ISO SOL       
> tau_t           = 0.1   0.1     
> ref_t           = 300   300     
> 
> pcoupl          = no
> 
> Greetings
> Lara
> 
> 
> 
> 
> 
> 
> 
> ----- Ursprüngliche Message -----
> Von: Peter C. Lai <pcl at uab.edu>
> An: Lara Bunte <lara.bunte at yahoo.de>
> CC: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
> Gesendet: 17:46 Montag, 24.September 2012
> Betreff: Re: [gmx-users] Water molecule can not be settled - mdrun error
> 
> Is this energy minimization or actual integrator = md?
> 
> On 2012-09-24 04:44:18PM +0100, Lara Bunte wrote:
> > Hello
> > 
> > Okay, I changed it to
> > 
> > nstlist         = 1
> > rlist           = 1.5
> > rlistlong       = 1.4
> > rcoulomb        = 1.5
> > coulombtype     = pme
> > vdw-type        = switch
> > rvdw_switch     = 0.8
> > rvdw            = 1.5
> > 
> > in my .mdp file and I got now this error:
> > 
> > step 1352: Water molecule starting at atom 8376 can not be settled.
> > Check for bad contacts and/or reduce the timestep if appropriate.
> > Wrote pdb files with previous and current coordinates
> > 
> > Are the .mdp Options still a problem?
> > 
> > 
> > I am really thankful for the big amount of help. Thank you.
> > Lara
> > 
> > 
> > 
> > 
> > 
> > 
> > ----- Ursprüngliche Message -----
> > Von: Peter C. Lai <pcl at uab.edu>
> > An: Discussion list for GROMACS users <gmx-users at gromacs.org>
> > CC: Lara Bunte <lara.bunte at yahoo.de>
> > Gesendet: 22:13 Freitag, 21.September 2012
> > Betreff: Re: [gmx-users] Water molecule can not be settled - mdrun error
> > 
> > On 2012-09-21 02:59:17PM -0400, Justin Lemkul wrote:
> > > 
> > > 
> > > On 9/21/12 1:31 PM, Lara Bunte wrote:
> > > > Hi Justin
> > > >
> > > > I used this settings except of vdw-type = switch and rvdw_switch = 0.8 and with this settings grompp gives me two notes and one of this notes is inconsistent:
> > > >
> > > > NOTE 1 [file pr.mdp]:
> > > >    For energy conservation with switch/shift potentials, rlist should be 0.1
> > > >    to 0.3 nm larger than rvdw.
> > > >
> > > > Because I thought rlist hast to be 1.2 and rvdw hast to be 1.2 for my CHARMM27 force field.
> > > >
> > > >
> > > 
> > > Increase rlist as suggested to accommodate the algorithm.  Since CHARMM does not 
> > > use charge groups (well, it uses single-atom charge groups) this isn't such a 
> > > big deal.  For a force field like Gromos96, it matters a lot more.
> > 
> > Actually rlist has to be equal to rvdw for this case (PME will complain if it
> > doesn't). I haven't had a water settling issue in a correctly setup system
> > with rlist = rvdw and a switched rvdw.  I do remember a bug in the code that
> > forgets rlistlong is specified.
> > 
> > > 
> > > >
> > > > My second note is:
> > > >
> > > > NOTE 2 [file pr.mdp]:
> > > >    The sum of the two largest charge group radii (0.079505) is larger than
> > > >    rlist (1.200000) - rvdw (1.200000)
> > > >
> > > >
> > > > which I sadly don't understand.
> > > >
> > > 
> > > http://www.gromacs.org/Documentation/Errors?highlight=errors#The_sum_of_the_two_largest_charge_group_radii_(X)_is_larger_than.c2.a0rlist_-_rvdw.2frcoulomb
> > > 
> > > -Justin
> > > 
> > 
> > I also get this note too, but the sum looks fine to me. If the sum > 0.15 then
> > it typically indicates chargegroups are being used, which they shouldn't for 
> > charmm-based forcefields, but in this case the distance shown is on the order
> > of a heavy-h bond. I think the note message is still related to rlist vs. 
> > rlistlong.
> > 
> > anyway, I routinely ignore both these notes and it hasn't given me problems
> > so far. I would still go bck to check the specific water that could not settle
> > and see what the other particles near it are since that is probably the root
> > of the problem. Also, we haven't been told what the results of the energy 
> > minimzation was...
> > 
> > -- 
> > ==================================================================
> > Peter C. Lai            | University of Alabama-Birmingham
> > Programmer/Analyst        | KAUL 752A
> > Genetics, Div. of Research    | 705 South 20th Street
> > pcl at uab.edu            | Birmingham AL 35294-4461
> > (205) 690-0808            |
> > ==================================================================
> 
> -- 
> ==================================================================
> Peter C. Lai            | University of Alabama-Birmingham
> Programmer/Analyst        | KAUL 752A
> Genetics, Div. of Research    | 705 South 20th Street
> pcl at uab.edu            | Birmingham AL 35294-4461
> (205) 690-0808            |
> ==================================================================

-- 
==================================================================
Peter C. Lai			| University of Alabama-Birmingham
Programmer/Analyst		| KAUL 752A
Genetics, Div. of Research	| 705 South 20th Street
pcl at uab.edu			| Birmingham AL 35294-4461
(205) 690-0808			|
==================================================================